edu.unh.sdb.datasource

Class ChomboDataSource

java.lang.Object

edu.unh.sdb.datasource.DataCollection

edu.unh.sdb.datasource.DataSource

edu.unh.sdb.datasource.ChomboDataSource

All Implemented Interfaces:

Indexable

public class ChomboDataSource
extends DataSource

Field Summary

Fields

Modifier and Type	Field and Description
int	defaultComponent

Fields inherited from class edu.unh.sdb.datasource.DataSource

fdlDescriptor, isActivated, name, wsName

Fields inherited from class edu.unh.sdb.datasource.DataCollection

attributeOrder, axisOrdering, axisWeights, bounds, dataOrder, dimensionality, numAttributes, pointOrder, recordDesc

Constructor Summary

Constructors

Constructor and Description
ChomboDataSource(java.lang.String name)
ChomboDataSource(java.lang.String name, FDLDescriptor fdld)
ChomboDataSource(java.lang.String name, java.lang.String fname)

Method Summary

Methods

Modifier and Type	Method and Description
void	activate() Activates the data source by opening the currently addressed file.
int	calculateNumElems(int lv, ISBounds bounds)
void	datum(Datum dtm, IndexSpaceID did, FieldIDMapper mp) Given an IndexSpaceID and FieldIDMapper, copy the values of the Datum at that position to the argument Datum.
void	deactivate() Deactivates the data source by closing the file and clearing all variables.
ISBounds	getBoxBounds(int lv, int boxNum)
byte[]	getBuffer()
int	getBufferSize()
double[]	getData(int lv, ISBounds bound)
java.lang.String[]	getDataComponents()
int	getDimensionality()
java.lang.String	getFilename()
int	getIteration()
int	getNumBoxes(int lv)
int	getNumLevels()
int	getNumValidBoxes(int lv, ISBounds inputSrcBounds)
ISBounds	getProbDomain(int lv)
int	getRefRatio(int lv)
double	getTime()
byte[]	makeByteBuffer(byte[] bytes, DSPartitionedStencil stencil) Creates a new byte buffer and returns it, based on the start and maximum levels specified, and the number of query boxes requested.
int	selectHyperslab(int lv, int dataspace, long[] start, long[] stride, long[] count, long[] block)
int	server_subblock(byte[] bytes, ISBounds inputSrcBounds, int byteOffset)
void	setComponent(int cmp)
void	setMaxLv(int mLv)
void	setStartLv(int sLv)
void	subblock(DataBlock theBlock, ISBounds dstBounds, ISBounds srcBounds) Reads a subblock defined by srcBounds into the region of the Datablock argument defined by dstBounds.
void	subblock(DataBlock theBlock, ISBounds dstBounds, ISBounds srcBounds, FieldIDMapper mp) Reads a subblock defined by srcBounds into the region of the Datablock argument defined by dstBounds.
void	useBytesOnly() When this method is called, this subblock methods of this collection will read data as bytes, without performing any type conversion.
int	writeHeader(byte[] bytes, DSPartitionedStencil stencil)
double[]	writeHyperslab(double[] data, int lv, long[] startData, long[] countData, int dataspace)

Methods inherited from class edu.unh.sdb.datasource.DataSource

checkActivated, clearCache, copyBestID, create, create, create, createRemote, createRemote, createRemoteClient, createRemoteClient, createRemoteDataSource, createRemoteDataSource, createRemoteDataSourceUDP, createRemoteUDP, createRemoteUDP, dumpData, equals, getFDLDescriptor, getMetadataCollection, getName, getStatistics, getValues, isActivated, main, setMetadataCollection, toString, toString

Methods inherited from class edu.unh.sdb.datasource.DataCollection

byteSize, computeOffset, computeOffset, copyBounds, createDataBlock, createDataBlock, createDataBlock, createDatum, createDatum, createDatum, createDatum, createDatum, createDatum, datum, datum, datum, datum, datum, datum, dim, getAttributeNames, getAxisOrdering, getAxisWeight, getAxisWeights, getBounds, getByte, getBytes, getBytes, getBytes, getBytes, getBytes, getBytes, getBytesByAttribute, getBytesByAttribute, getBytesByPoint, getBytesByPoint, getDataOrder, getDimensionsArray, getDouble, getDoubles, getDoubles, getDoubles, getDoubles, getDoubles, getDoubles, getDoublesByAttribute, getDoublesByAttribute, getDoublesByPoint, getDoublesByPoint, getFloat, getFloats, getFloats, getFloats, getFloats, getFloats, getFloats, getFloatsByAttribute, getFloatsByAttribute, getFloatsByPoint, getFloatsByPoint, getInt, getInts, getInts, getInts, getInts, getInts, getInts, getIntsByAttribute, getIntsByAttribute, getIntsByPoint, getIntsByPoint, getLowerBoundsArray, getNumAttributes, getRecordDescriptor, getShort, getShorts, getShorts, getShorts, getShorts, getShorts, getShorts, getShortsByAttribute, getShortsByAttribute, getShortsByPoint, getShortsByPoint, getStorageType, getUpperBoundsArray, getValues, getValuesByAttribute, getValuesByPoint, longVolume, setAxisOrdering, setBounds, setRecordDescriptor, size, subblock, subblock, subblock, subblock, subblock, subblock, subblock, subblock, subblock, subblock, volume

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

defaultComponent

public final int defaultComponent

See Also:

Constant Field Values

Constructor Detail

ChomboDataSource

public ChomboDataSource(java.lang.String name)

ChomboDataSource

public ChomboDataSource(java.lang.String name,
                java.lang.String fname)

ChomboDataSource

public ChomboDataSource(java.lang.String name,
                FDLDescriptor fdld)

Method Detail

useBytesOnly

public void useBytesOnly()

When this method is called, this subblock methods of this collection will read data as bytes, without performing any type conversion. This is meant to be used by servers, since they send raw bytes over the network anyway, and any conversion is wasted effort. Since Chombo files are already read as bytes, we override this method, and do nothing.

Overrides:

useBytesOnly in class DataCollection

activate

public void activate()

Activates the data source by opening the currently addressed file.

Overrides:

activate in class DataSource

deactivate

public void deactivate()

Deactivates the data source by closing the file and clearing all variables.

Overrides:

deactivate in class DataSource

datum

public void datum(Datum dtm,
         IndexSpaceID did,
         FieldIDMapper mp)

Description copied from class: DataCollection

Given an IndexSpaceID and FieldIDMapper, copy the values of the Datum at that position to the argument Datum. TODO Define error conditions

Specified by:

datum in interface Indexable

Specified by:

datum in class DataCollection

getBoxBounds

public ISBounds getBoxBounds(int lv,
                    int boxNum)

getDataComponents

public java.lang.String[] getDataComponents()

getDimensionality

public int getDimensionality()

getFilename

public java.lang.String getFilename()

getIteration

public int getIteration()

getNumBoxes

public int getNumBoxes(int lv)

getNumLevels

public int getNumLevels()

getProbDomain

public ISBounds getProbDomain(int lv)

getRefRatio

public int getRefRatio(int lv)

getTime

public double getTime()

setStartLv

public void setStartLv(int sLv)

setMaxLv

public void setMaxLv(int mLv)

setComponent

public void setComponent(int cmp)

makeByteBuffer

public byte[] makeByteBuffer(byte[] bytes,
                    DSPartitionedStencil stencil)

Creates a new byte buffer and returns it, based on the start and maximum levels specified, and the number of query boxes requested.

Parameters:

startLv - Starting refinement level chosen

maxLv - Ending refinement level chosen

queries - Query box bounds

Returns:

Bytes array large enough to hold the requested data

writeHeader

public int writeHeader(byte[] bytes,
              DSPartitionedStencil stencil)

calculateNumElems

public int calculateNumElems(int lv,
                    ISBounds bounds)

server_subblock

public int server_subblock(byte[] bytes,
                  ISBounds inputSrcBounds,
                  int byteOffset)

getBuffer

public byte[] getBuffer()

Returns:

The data buffer currently stored in the data source. This is typically the most recently used buffer, whether a header was written or server_subblock was called to write data.

getBufferSize

public int getBufferSize()

Returns:

The size limit of the previously created data buffer

getData

public double[] getData(int lv,
               ISBounds bound)

writeHyperslab

public double[] writeHyperslab(double[] data,
                      int lv,
                      long[] startData,
                      long[] countData,
                      int dataspace)

selectHyperslab

public int selectHyperslab(int lv,
                  int dataspace,
                  long[] start,
                  long[] stride,
                  long[] count,
                  long[] block)

getNumValidBoxes

public int getNumValidBoxes(int lv,
                   ISBounds inputSrcBounds)

subblock

public void subblock(DataBlock theBlock,
            ISBounds dstBounds,
            ISBounds srcBounds)

Description copied from class: DataCollection

Reads a subblock defined by srcBounds into the region of the Datablock argument defined by dstBounds.

Specified by:

subblock in interface Indexable

Specified by:

subblock in class DataCollection

subblock

public void subblock(DataBlock theBlock,
            ISBounds dstBounds,
            ISBounds srcBounds,
            FieldIDMapper mp)

Description copied from class: DataCollection

Reads a subblock defined by srcBounds into the region of the Datablock argument defined by dstBounds. The FieldIDMapper argument determines the mapping between datums in this DataBlock and datums in the argument DataBlock. It is legal to pass a null for the FieldIDMapper argument which means that all attributes are to be extracted.

Specified by:

subblock in interface Indexable

Specified by:

subblock in class DataCollection